Whether McCoy is a replicant or not is entirely up to you, the player. Hints are given that suggest he is, while there are also hints that contradict this notion. Is he human, or is he a replicant – or is he a human who happens to be on the reps’ side (a sympathizer)? You decide.
Reportedly, there is a way to be sure: at the end, in the stolen moon bus, you see the original copy of a picture that had both McCoy and the other replicants on it. If you’re on the picture, you ARE a replicant. If you’re not, well, then you were tricked.